Following the Stars
by GeniusMadness
Summary: The Doctor does return for Amelia Pond in "5 minutes" and they are set to embark on their own adventures when the TARDIS malfunctions and finds itself on the USS Enterprise click for longer summary! Features Het & Slash, all ships and warnings inside...
1. Chapter 1

**Title:** Following the Stars – Chapter 1  
**Fandom(s):** Star Trek XI/11th Doctor Who crossover  
**Pairing(s):** Established: Spock/Uhura and Scotty/Gaila * Eventual: Sulu/Chekov, Kirk/Bones, Doctor/Jack Harkness, variations of Kirk/Bones/Doctor/Harkness and mentions of past Jack/Ianto  
**Rating:** PG-13 with eventual R or NC-17 **Warnings: ** AU, Slash, Character Death, angst, fluff, and possible moments of terror/suspense  
**Summary:** The Doctor does return for Amelia Pond in "5 minutes" and they are set to embark on their own adventures when the TARDIS malfunctions and finds itself on the USS Enterprise. The crew doesn't know what to make of their unexpected guests and the Doctor realizes he might have been brought here for a reason, to try to save the crew…from them.  
**Disclaimer:** I own NOTHING! Everything belongs to creative people, companies, (etc) that are not me and I make no money from this venture…trust me. Also: All mistakes are my own and I take full responsibility for them  
**Author's Note:** Timelines: Doctor Who follows canon up until Season 5/Episode 1, the events of Torchwood happened through CoE and as for Star Trek; it's a few months after the end of the film. Hopefully this is clear, if not, give me a heads up!

"You came back!" Amelia Pond shouted with glee, as she lifted herself off the hard suitcase she was sitting on, and threw herself into the arms of one very surprised Doctor.

"I said I'd only be five minutes…" The Doctor answered, while awkwardly returning the little red-headed girl's hug.

"That's what everyone says," Amelia replied, repeating the statement she said to the Doctor right before he left.

"Well," started the Doctor as he went to retrieve the human girl's suitcase, while extending his other hand for the child to take, "I'm not everyone," he stated with a wink.

"No, you're not," that fact seemed to make the seven-year old very happy as she followed the Doctor into the blue police box, his spaceship.

"Oh…wow!" Amelia exclaimed upon entering, "It-It's so –" The Doctor cut in and said, "Much bigger on the inside?" having heard the phrase quite often from past companions, when first seeing the inside of the TARDIS.

"Well, _yeah_ that too!" Amelia exclaimed excitably but with a hint of 'well obviously!' before continuing, "What I mean to say is that it's," she took a deep breath before finishing, "so amazingly cool!" Amelia let go of the Doctor's hand to look around in awe and walk over to take a peek at the console, "What's this?"

"Oh uh umm nothing, really, just don't touch anything please," The Doctor replied hastily, putting down Amelia's suitcase and running over to the console to hit at several buttons, throwing switches with seemingly random abandon.

Amelia curiously looked at The Doctor before asking, "What's wrong?"

"It's a bit difficult to say, it looks like something is wrong with the TARDIS," The Doctor replied, while looking under the console and changing up some of the wires.

"Is that what this is called, a TARDIS?" Amelia asked looking around in amazement once more.

"Yep, stands for Time and Relative Dimension(s) in Space. But right now it's acting a bit odd, though no worries! A quick trip around the moon should help energize it and then we can go wherever or whenever you'd like!"

Amelia Pond looked at The Doctor with wide brown eyes, "Are you serious?"

"Of course I am!" The Doctor looked up with a big smile, arms stretched out excitably, while he hopped down to meet Amelia.

"Tell me, Pond, the universe is ours…what would you like to do first?"

Amelia smiled gently and tugged on one of the elbow patches on The Doctor's brown tweed jacket lightly, before replying joyfully, "I'd kind of like to see what home looks like in the future, if you can do that?"

The Doctor just grinned widely and replied, "I'm The Doctor! I can do anything! How does the 32nd century sound?"

Amelia bounced on the balls of her feet happily while saying, "That sounds wonderful, Doctor!"

"Then what are we waiting for? Let's go!"

Amelia clutched at The Doctor's arm and asked with jovial disbelief, "This is really happening? I can go with you?"

"Absolutely, you can trust me! You do, don't you?" The Doctor asked with slight hesitation.

By all means, Amelia knew this was a man she had just met. A man, who crashed into her garden, came out of this peculiar box soaking wet and asking for an apple, and then deciding he didn't like anything she made for him to eat except fish fingers dipped in custard. But he was also the man, who fixed the scary crack in her wall with no problem and paid her more attention than anyone had since her parents died. Amelia decided that while The Doctor was inarguably odd, he was someone she could trust.

"I trust you," Amelia stated bravely.

"Fantastic!" The Doctor shouted before running over to the console and punching in codes haphazardly, at least to Amelia's eyes, and yelling out, "Hold on tight, Pond!"

Amelia gripped the handle bar just in time, before the TARDIS launched with a start and she had to wonder if the TARDIS was always like this, or if it was just because it was acting "slightly odd" right now?

Her suitcase was sliding back and forth along the TARDIS's floor and Amelia was focused on her hands which were holding onto the bar, her knuckles becoming an even paler white, before the TARDIS made a weird sound and landed with a loud 'bang' and a 'thud'.

"Huh, that didn't sound too good," The Doctor stated, waving his hands wildly over the console which had started to smoke and spark a bit.

"Are we there? Did we make it?" Amelia asked, while poking her head up to look at The Doctor.

"Hmm think so? We'll step out and discover that in a minute. Problem is I think the TARDIS needs some repairs."

Amelia could tell The Doctor tried not to show that he was concerned, probably for her sake. So she just pulled on The Doctor's sleeve and said hopefully, "Well let's hope people in the 32nd century are nice then, huh? Maybe they can help us?"

The Doctor's lips quirked a little into a small smile, finding the child's innocence and optimism refreshing.

"Indeed, let's find out!" The Doctor stated before pausing and saying, "Actually, wait here. I'm going to check what's outside first." He was so used to traveling with adults, he had to remember she was just a little kid and he was responsible for her.

"Why? Do you think it could be dangerous?"

"Possibly…"

"Really?"

"Well don't act so excited about that! I'm serious here!" The Doctor finished with a pout, which honestly just made Amelia want to giggle.

"Okay, fine, fine." He replied dramatically, "We'll go together, but stay close to me!"

Amelia did a mock salute and held out her hand, wiggling her fingers a little, which the Doctor took. He patted his jacket pockets mentally checking for: sonic screwdriver, TARDIS keys, and everything else of importance, before opening the door to find…

"This is an engine room," Amelia stated with some confusion.

"Yeah, I wasn't expecting that either."

They stood there for a few minutes, Amelia waiting to see what The Doctor would do, and The Doctor trying to figure out exactly what he should do, when they both heard a moan coming from a slight distance away.

"Doctor, what was that? It sounds like someone is in pain."

"I don't know, just…wait here I'm going to check it out. I'll be right back."

The Doctor ran forward and around a few corners, but abruptly skirted to a stop at the sight before him. There was a human male pinning a gorgeous green-skinned girl to the wall in a dark corner. The man was kissing along her flat belly and one of his hands slipped into the girl's white lacy underwear, to which she gave a husky, "Oh YES! Ooh right there, you're al-always so good, Scotty."

"Mmm, always, you say?" The man teased, rising up slightly to lean over and kiss her on the lips, when just then, the man looked up and spotted the Doctor. The Doctor panicked and backed into one of the large pipes behind him, which caused the female to shriek and for the two of them to pull apart and quickly grab at their discarded articles of clothing. The moment between the couple was ruined, and neither one was too amused by that fact.

"Good Lord, man! Can't ya see we are wanting some privacy here? And who are ya anyway?"

"Uhhh, sorry so…yeah, my apologies," The Doctor replied, with a blush upon catching a human male in the middle of a sex act with a female Orion. Also, how_ did_ she bend her legs like that?

The pretty Orion was bending over to pick up her clothes, while the human male stepped in front of her, giving her a little sense of privacy, and was pulling up his black pants with a very angry and disgruntled look on his face before asking yet again, "As I said, who are ya? Does the captain know you're down here?"

"I'm The Doctor and errr, I don't know if the Captain knows I'm here?"

The man was tugging on his undershirt now as he looked at him quizzically, "You…don't know?"

"Doctor where are you?" Amelia called out, "Doctor?"

"I'm here Amelia! Just follow my voice, you can come over now." The Doctor was a little embarrassed to admit that he forgot she was there. But considering what he just saw, well, it threw him a bit. He also had to silently thank every deity in the known universe that he had told Amelia to wait for him, until he had a look first.

"And what the bloody hell is this? You have your girl with you here, too?"

"Uh, a girl, not exactly my girl…" at the man's look of utter disbelief, The Doctor finished, "This isn't coming out right. Sorry, this isn't the best way to met."

"I would say not," the beautiful female spoke for the first time, scarlet hair slightly messy, but now completely redressed. Thankfully, as Amelia had joined them now, and the Orion continued, "I'm messaging Chekov to call the Captain."

"Wait, wait! Before you do that, I just want to know where or actually, _when _am I?"

The couple stared at him as the four of them settled into an uneasy silence.

"When are you? When? Not this again," The man, Scotty, answered.

"Not this again? Hold on a second…"

"No, you hold on a second. What are you?"

"I'm a Time Lord."

"You're not human?" Amelia asked, a little shocked, "You look human."

"Well, you look Time Lord. Time Lords came first, you know. But anyway, shut up!"

They all continued to look at him, perplexed and bemused.

"Just, tell me what century I'm in."

"The 23rd century," the Orion spoke up again, confused.

"Oops"

"Oops?" Amelia asked, for the first time a little cautiously.

"It would seem I mixed up the order of the 2 and 3 button, but that's no matter! We're here now in the 23rd century aboard the…"

"USS Enterprise?" the Orion answered for him again.

"Oh, that's brilliant! And what's your name?"

Scotty impatiently interrupted, raising his voice and saying, "Don't! Stop answering him, he's an intruder, he could be dangerous!"

"Traveling with a child? C'mon he's…"

"Well, I don't know! I mean, how did he even beam aboard this ship without anyone knowing about it? This is crazy; I'm messaging the captain or someone that can get a hold of him."

"That won't be necessary," The Doctor turned around to see a uniformed officer heading towards them, this one wearing a blue shirt.

"Are you the captain?

"No, but I'm the commanding first officer. How did you beam aboard this ship?"

"Well you see, I…" The Doctor suddenly started to get a horrible headache and began to feel slightly faint, but shook his head and continued, "It's kind of complicated. But, basically I'm The Doctor," to which he gave a small, awkward wave as way of introduction, "and this is Amelia Pond," he gestured to the young girl beside him, who also gave a timid little wave, "and we were heading to the 32nd century but my spaceship was a little broken…well, it is fully broken now. But anyway, we kind of landed here, by accident. And we'd leave, except we can't."

The stern looking first officer quirked an eyebrow, stepping closer to the group and The Doctor noticed for the first time, the pointed ears, slanted eyebrows and realized he was Vulcan. What kind of ship did he land on, exactly? What ship inhabited Orions, Vulcans, and humans, except…?

"Wait a minute, this ship; this crew is part of Starfleet?"

"Yes, and I demand to know –"

"Oh that's great! Wonderfully brilliant, because you can actually help me and –" The Doctor's headache worsened and his legs started to get shaky.

"Doctor, are you alright?" Amelia asked voice full of concern.

"Yeah, I'm fine, it's just, you know…" and then The Doctor's legs gave way, and he sagged against one of the water pipes before falling to the floor.

"Doctor, oh my god, Doctor!" Amelia's voice echoed and faded into his subconscious.

The Doctor's last thought before passing out, was how he thought this regeneration was going to be different. You know, by not being rendered unconscious or otherwise greatly incapacitated after the change, but really? He should have known.

So, what do you think of it so far? Is it worth continuing? Love it or hate it, please REVIEW! It makes the writer happier than you'll ever know


	2. Chapter 2

**A/N:** I can't apologize enough for my year and a half hiatus from writing. Life happened, I lost my muse…but I've finally found it! I won't leave you stranded for so long again and this story will be written! Infinite thanks to all of you who have not given up on me.

**Reminder on the Time Line: **

Star Trek XI – This one is the most simple, it is a few months after the movie.

Doctor Who - Follows canon up until Season 5/Episode 1. This is important, there is and never will be a River Song. Time has changed now that the Doctor returned for Amelia Pond.

Torchwood – All the events happened through Children of Earth. Miracle Day never happened.

* * *

The Doctor opened his eyes slowly and then closed them against the bright light. He felt tired, grungy, and like he was going to be sick soon. He tried sitting up when he heard a man's voice say, "Here let me help. Are you thirsty?"

The Doctor nodded wearily and tried opening his eyes again to see a man in a blue shirt, not unlike the Vulcan's shirt he had seen before. From before…and then the memories came rushing back in full force.

The Doctor bolted up, "Amelia! Is she okay?"

"Steady man! The girl is fine, just fine. She'll be very happy to know you're awake. Calm down and drink this," the man replied as he handed The Doctor a glass of water.

"I need to see her," The Doctor persisted trying to get up but finding he was hooked up to an IV, "just how long have I been here exactly? And where am I again?"

"You're in the medical bay aboard the USS Enterprise. You've been here almost a week."

The Doctor winced at this news and silently cursed the whole regeneration process again.

"I'm just going to do a short check up, you should be able to get up and walk around today." The man in blue gently removed the IV and changed the bandages on his hand. The Doctor didn't even remember hurting it but he must have when he passed out.

"I'm Dr. McCoy by the way. Sorry I forgot to properly introduce myself. You're a Doctor too from what I hear?"

"What? Uh no, I'm _the_ Doctor not_ a_ Doctor."

McCoy gave him a very perplexed look before reaching for his stethoscope and placing it over The Doctor's hearts.

"Both heartbeats are regular," McCoy said mostly talking to himself, checking the clipboard attached to the Doctor's bed.

If McCoy wasn't freaked out by hearing two hearts then it meant he'd pretty much seen and heard it all. It made sense if he was a member of Starfleet, they were the best and this made The Doctor feel a little better about his predicament.

"Are you feeling anymore headaches?"

"No I'm fine really. Listen," The Doctor took a deep breath, "I need to see Amelia. And yes my name is The Doctor. I know it is confusing to humans but really simply 'Doctor' will do."

"Doctor Who?"

"Just," the Time Lord paused and said carefully, "The Doctor."

* * *

McCoy left the room to give the Doctor some privacy to change into his now clean clothes and wash up. Dr. McCoy had certain quirks and personality traits that reminded the Doctor of somebody. When he realized that somebody was Martha Jones he tried not to think about it.

The Doctor readjusted and checked his bow tie in the mirror, combed his hair, and went out to meet McCoy.

"Dinner will be soon. Best bet is that Amelia will be in the dining hall then with the rest of the crew. Captain would like to see you too, of course."

The Doctor nodded and followed alongside McCoy for a couple minutes before asking, "Amelia was well taken care of? Did she ask for me?"

"She visited you every morning. Amelia was very concerned. Said that you're her Uncle?"

The Doctor grinned. That was certainly the safest lie to tell.

"Yes."

McCoy nodded and continued his response, "And don't worry. The crew absolutely adore Amelia and she was very well looked after," McCoy chuckled, "She's full of life, that one."

It was the first time the Doctor actually saw McCoy quirk a smile. The set of doors in front of them swooshed open into a decent sized dining hall. Lots of people in red shirts, though there were some blue and gold scattered among them too.

Amelia spotted them right away, "Doctor! You're awake! You're okay!" she exclaimed loudly as she ran into the Doctor's open arms for a huge hug.

"I was so worried you wouldn't be okay. I thought you might…leave me." The last part was said in a pained whisper.

"I'm so sorry Amelia. It was the whole regeneration process, I should have known better. I won't leave you like that again."

Amelia just nodded into the Doctor's chest and he knew she was trying not to cry in front of everyone. The Doctor felt horrible putting her through that. And he wondered not for the first or last time, if bringing a child on his adventures wasn't a silly and selfish thing to do.

Amelia pulled back from the hug a little, gave a small shaky smile and said, "I saved you some custard. Just in case. They didn't have any fish sticks though."

The Doctor didn't know what to say. So he leant down and kissed Amelia's forehead before murmuring, "Thank you" and let Amelia take his hand and lead him to a nearby table.

* * *

As the two of them approached the table the Doctor could see a young and very handsome man wearing a gold shirt. He looked like he had a great sense of humor as he was laughing heartily at something the Asian male sitting across from him had said. But he seemed arrogant. Kind of like another Captain he knew.

The Doctor didn't really like that the crew was reminding him of past companions.

"I swear that's what Chekov said!" The Doctor could hear the Asian man exclaim, "You should have seen Scotty's face!"

"You expect me to believe our innocent Chekov said that? I don't believe you."

"He's not that innocent, Captain. He's eighteen now and has been through almost as much as us."

"Oh I see. Not that innocent now, eh? Really Sulu…" the young man gave a salacious wink, "you didn't waste any time."

Sulu's face turned a deep scarlet and he looked like he was trying to utter a reply when the Captain looked up and said, "Oh hello Amelia! Glad to see your uncle is finally awake and doing well."

He turned to look at the Doctor. "You gave us quite a scare," he said as he stood up to shake the Doctor's hand. "Please have seat," the Captain signaled with a wave of his hand, "We have much to talk about."

"Of course…do you have another name other than Captain?"

"I do. Name's Jim Kirk. But you still have to call me Captain, Doctor. " Kirk finished with a smirk.

Amelia sighed loudly and asked, "Are you both going to talk for a long time? Can I play with Chekov? He's teaching me how to play chess!"

Sulu picked up his tray and said, "I'll join you Amelia. They're going to talk about boring adult stuff."

At the last part Sulu made a face and Amelia giggled as she picked up her tray and went to follow Sulu, telling the Doctor she'd check up on him soon.

"Thanks Amelia. How would I survive without you?" The Doctor only half joked.

"Ohhh I don't know," Amelia sighed with an exaggerated manner. And though she acted like a little adult sometimes she still had the temperament of a child as she skipped ahead and called back, "Come on! Are you ready to play with Chekov, Sulu?"

"Yeah Sulu," Kirk cut in and subtly licked his lips, "Are you ready to play with Chekov?"

"Piss off, Captain."

* * *

Jim Kirk was young but experienced being a Captain. He was decisive and extremely loyal to his crew. He asked the Doctor numerous questions, all of which the Doctor was more than happy to answer. When he seemed to pass the 'not a danger to the crew' test Kirk seemed to let up on his questioning and just replied, "Well Doctor. Our chief engineer has been giving your ship a look over to see if he can fix her. Scotty says it is a real mess in there."

"What?" the Doctor dropped his spoon with a loud 'clang' and cleared his throat, "No one can fix the TARDIS but me. I'm the only one who understands her. Also I'd appreciated no one touching her but me if you don't mind."

"Listen Doctor," Kirk said with a calm yet unmistakably stern voice, "Scotty is the best engineer in the galaxy. You should be honored he is using the free time from his duties to help you. Be honest, you need our help. Take it."

The Doctor hated to admit that Kirk was right. He needed all the help he could get to repair the TARDIS and get off this ship. There was still something unsettling about the whole situation. The Doctor wished he could just understand _why _that was.

"I thank you for your help and accept. But I don't know if Scotty and I can work well together."

Kirk quirked an eyebrow, "And why's that?"

"Well because I caught him…in an intimate position with that female Orion. I think he might understandably still be a bit upset about that."

Kirk flashed the Doctor that teasing grin of his again, "You don't say? Hmmm that's very interesting."

"You didn't know," he said and berated himself for telling, "Please forget what I said. It wasn't my place to tell."

"Now Doctor, what kind of Captain would I be if I didn't look after the well being of my crew? This is all stuff that I need to know."

"That seems highly unlikely if you ask me, Captain."

The Doctor looked up to see the Vulcan that he met upon first arriving. The Vulcan's head was slightly titled as if in constant thought and his arms were folded behind his back as he continued, "It would seem to me the need for that particular knowledge would steam from personal curiosity then actual knowledge needed to perform the Captain's duties concerning one's emotional or physical health of his or her crew. I would personally advise against invading one's personal information, especially that of a romantic or sexual nature."

"Spock my friend," Kirk said jovially seemingly ignoring or not caring what the Vulcan just said, "Have you met our guest?"

"Briefly," Spock answered curtly.

"That's right. You advised against keeping him on board if I remember correctly."

"I still stand by that statement, Captain."

"I understand your concerns but he and his niece are here to stay now, for the time being at least."

The Doctor silently watched the exchange between the Captain and his first commanding officer. He remembered Spock introducing himself as such upon their first meeting. The Doctor couldn't understand how they worked so closely together. They were clearly opposites.

"We are 29 days away from Sector 87 where our mission is to take place. The mission is too dangerous for a child and I don't want our mission to be…" he looked at the Doctor, "compromised."

The Doctor paled considerably and said in a hushed whisper, "Sector 87?"

Kirk and Spock gave each other a sideways glance before Kirk responded, "Yes. There have been reports of ships disappearing there. Our mission from Starfleet is to investigate the surrounding area. Is there a problem?"

"No!" the Doctor said harshly before clearing his throat and lowering his voice, "I mean no. Sorry no there's not a problem. I'm just…tired. It's been a long day."

"Sure of course," Kirk said studying the Doctor, "Spock here can lead you to the quarters you'll be sharing with your niece."

The Doctor stood up abruptly, "Thank you for your hospitality, especially in caring for Amelia. I promise I will work diligently to fix the TARDIS so we can leave soon without further taking up your time and generosity."

* * *

The Doctor laid on one of the double beds as Amelia paced their room, talking animatedly, "And then Chekov won the game of course. But he said that I am improving! Oh and you haven't met Uhura yet, have you? She is so sweet. And pretty! I think Spock and her make such a nice couple and…"

Amelia paused looking at the Doctor, "Is something wrong?"

The Doctor turned his head to look at her, "I'm just thinking."

"Oh. Well," Amelia jumped lightly at the end of his bed, "What about?"

The Doctor's head started to hurt again, "Nothing in particular."

"Do you like the crew, Doctor?"

"They seem nice enough. I certainly respect them all though. They took good care of you."

"You too Doctor, don't forget!"

The Doctor smiled lightly and tried to hide the hurt from his eyes, "I won't."

"Can we stay with them for awhile? I think if you got to know them better, you'd like them a lot!"

The Doctor didn't want to get to know them better though. It would be too painful. The USS Enterprise Sector 87 mission, that's how he heard of them. How could he forget? Everyone knew that mission. Their names were in history books across several galaxies. They saved the entire universe.

But it was no use getting to know or like any of them when they were all going to die.

"Amelia," The Doctor choked out emotionally, "we're leaving as soon as the TARDIS is fixed."

* * *

I KNOW. Short chapter and a cliffhanger after a super long hiatus, don't worry though! The muse is finally working ((pets muse)) both reviews and criticisms help feed the hungry little beast so it knows what you like. I hope you are all enjoying it so far!


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